First is the condensation that forms on the inside of the car. Think of a glass of ice water sitting outside on a warm summer day. Condensation is going to form on the outside of the glass because it is so warm. I've even seen condensation form on the outside of house windows on a hot humid summer day when the air conditioner is on inside. Same concept with your car. When it is cold and snowy outside, you have the heat cranked up inside your car. This creates condensation, in addition you create more moisture when you are breathing and when you get in your car with snow on your shoes which melts and then evaporates. Cars have vents near the rear to help keep the air flow going through the vehicle, however that is not enough in the civic's case. Also the civic only has this vent on the drivers side below the tail light, not like many vehicles that have them on both sides and even in the door jambs sometimes. This creates condensation build up on the inside of your rear quarter panels. It drips down and collects around the inside of the wheel well. This is how the rust begins where the rear bumper meets the wheel well, the rust starts inside and eats its way through, until you see a tiny bubble or two form on the outside of your fender's paint. Condensation also drips down the front of the wheel well and sits in the inner rocker panel area. Fortunately, the inner rocker panel space has drain holes in the bottom but can still rust. This area is behind the plastic side skirts so you usually wouldn't know if there is rust.
Second cause of rust is the rubber strip honda puts on the inner fender lip. People rip these off and throw them away because they retain water and road salt. These rubber strips also prevent rock chips which can lead to rust. So instead of taking them off and throwing them away, clean the whole area and inside of the strip & let everything dry, apply body sealer, silicone or similar calk to the inside of the strip and put it back on. Now you have protection from rock strips, and you're keeping the moisture out.
I have a 92 hatchback. I bought it with 100k miles in summer of 2000, it had only one tiny bubble in the paint on the passenger fender. In fall of 2005 and 177k mi the body wasn't so pretty. The car has always been driven in winters. I love how the car handles, so I decided to fix the body. I had many of the tools, or was able to borrow them.
I bought a Lincoln SP135 MIG welder & accessories which would pay for itself on this job. ($430 shipped brand new from ebay)
A compressor & air tools made life easier too. A cutoff tool, angle die grinder, and 5" sander were used. The sander wasn't as nessacery though.
I also used an electric 4.5" grinder and drill, both of which are needed. The drill is used to drill out the spot welds so have some sharp bits. Also have a couple wire wheel attachments for the drill to remove the factory body sealer. Other tools were vise grips, c-clamps, quick grip clamps, and some special clamps to hold on the panel for welding (although I found it easier to hold the panel by hand to tack it on)
DISCLAIMER: I'm not liable for anything you do to injure yourself. Always wear eye protection and other needed pretection when cutting metal and welding. Always use jackstands! I am by no means an expert at body work, my civic was my first attempt at doing so. There may be a better way to do this, but I created this page to show how an average joe can do this by themselves, in their driveway. Do not attempt to do this yourself if you are not 100% confident. Rather than injure yourself or mess up your repair, it may be worth your time/$$ to pay a professional to repair your honda.
Companies now offer the lower rocker panels as well, so you won't have to fabricate your own out of sheet metal like I did. That's going to save a ton of time!